Variant report

Variant	rs428870
Chromosome Location	chr21:46525938-46525939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46525704..46527706-chr21:46528472..46530391,2	K562	blood:
2	chr21:46221400..46223268-chr21:46524948..46526484,2	MCF-7	breast:
3	chr21:46524740..46528756-chr21:46537470..46542914,5	K562	blood:
4	chr21:46523822..46526157-chr21:46543907..46545528,2	MCF-7	breast:
5	chr21:46525858..46528756-chr21:46540058..46542914,3	K562	blood:
6	chr21:46492354..46499042-chr21:46517406..46531809,25	K562	blood:

Variant related genes	Relation type
ENSG00000184787	Chromatin interaction
ENSG00000236519	Chromatin interaction
ENSG00000235374	Chromatin interaction
ENSG00000268856	Chromatin interaction
ENSG00000197381	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10222166	0.85[JPT][hapmap]
rs12482868	0.82[ASN][1000 genomes]
rs12482954	0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs12483020	0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs12483115	0.98[ASN][1000 genomes]
rs12483279	0.88[CHD][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs12483312	0.85[ASN][1000 genomes]
rs12483758	0.85[ASN][1000 genomes]
rs12627151	0.85[JPT][hapmap]
rs1556316	0.92[JPT][hapmap]
rs1556318	0.85[JPT][hapmap]
rs1556319	0.85[JPT][hapmap]
rs17004734	0.92[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs17004739	0.87[CHD][hapmap];0.92[JPT][hapmap]
rs17004743	0.85[JPT][hapmap]
rs17004748	0.85[JPT][hapmap]
rs2838774	0.88[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs2838776	0.83[ASN][1000 genomes]
rs2838786	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs2838789	0.81[CEU][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap]
rs2838792	0.85[JPT][hapmap]
rs2838801	0.84[JPT][hapmap]
rs2838802	0.85[JPT][hapmap]
rs2838809	0.85[JPT][hapmap]
rs2838810	0.85[JPT][hapmap]
rs2838811	0.81[JPT][hapmap]
rs2838812	0.85[JPT][hapmap]
rs2838816	0.85[JPT][hapmap]
rs3178603	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs367228	0.85[JPT][hapmap];0.83[ASN][1000 genomes]
rs372173	0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs372549	0.85[JPT][hapmap]
rs3746976	0.85[JPT][hapmap]
rs3788154	0.85[ASN][1000 genomes]
rs3788155	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs3788156	0.88[CHD][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs3788163	0.92[CHD][hapmap];0.92[JPT][hapmap]
rs3788164	0.92[JPT][hapmap]
rs3788169	0.85[JPT][hapmap]
rs3788181	0.85[JPT][hapmap]
rs386528	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs390504	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs391834	0.91[ASN][1000 genomes]
rs406551	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs412626	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs412666	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs421643	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs423726	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs431529	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs431666	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs431775	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs437286	0.92[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs439884	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs442380	0.92[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs447656	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs454052	0.92[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6518215	0.85[JPT][hapmap]
rs6518216	0.85[JPT][hapmap]
rs6518218	0.85[JPT][hapmap]
rs7275205	0.85[ASN][1000 genomes]
rs7275931	0.81[ASN][1000 genomes]
rs7277143	0.85[JPT][hapmap]
rs7279808	0.82[JPT][hapmap]
rs7281718	0.80[ASN][1000 genomes]
rs7283317	0.85[JPT][hapmap]
rs7283619	0.83[ASN][1000 genomes]
rs731248	0.92[JPT][hapmap]
rs8129934	0.92[JPT][hapmap]
rs8130862	0.83[JPT][hapmap]
rs8132752	0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs8134889	0.92[JPT][hapmap]
rs870145	0.88[CHD][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs870350	0.83[ASN][1000 genomes]
rs870351	0.92[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv3541	chr21:46496415-46536629	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv531546	chr21:46504151-47411772	Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs428870	MX2	cis	parietal	SCAN
rs428870	C21orf33	cis	cerebellum	SCAN
rs428870	DNMT3L	cis	parietal	SCAN
rs428870	KRTAP10-7	cis	cerebellum	SCAN
rs428870	HSF2BP	cis	parietal	SCAN
rs428870	SLC19A1	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46513200-46529200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr21:46516400-46549400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr21:46519400-46526800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr21:46521200-46527000	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr21:46521200-46528800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr21:46521400-46526400	Enhancers	Adipose Nuclei	Adipose
7	chr21:46521600-46526400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr21:46521600-46526800	Genic enhancers	HSMM	muscle
9	chr21:46521800-46526600	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr21:46521800-46526800	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr21:46522000-46526400	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr21:46522000-46527000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr21:46522200-46527200	Enhancers	Colon Smooth Muscle	Colon
14	chr21:46522600-46538600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr21:46522800-46529600	Weak transcription	NH-A	brain
16	chr21:46523000-46526200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr21:46523000-46529200	Weak transcription	Colonic Mucosa	Colon
18	chr21:46523000-46529400	Weak transcription	NHLF	lung
19	chr21:46523000-46532600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr21:46523000-46548200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr21:46523200-46529000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr21:46523400-46526800	Enhancers	Fetal Heart	heart
23	chr21:46523400-46527000	Enhancers	Primary T cells from cord blood	blood
24	chr21:46523600-46526200	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr21:46523600-46526800	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr21:46523800-46526000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr21:46523800-46527000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr21:46524000-46526400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr21:46524000-46527200	Enhancers	HSMMtube	muscle
30	chr21:46524200-46527000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr21:46524400-46526000	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr21:46524400-46526600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr21:46524600-46528800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr21:46524600-46529200	Enhancers	Primary B cells from cord blood	blood
35	chr21:46524800-46526000	Weak transcription	Psoas Muscle	Psoas
36	chr21:46524800-46526200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr21:46524800-46526200	Weak transcription	Esophagus	oesophagus
38	chr21:46524800-46526200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr21:46524800-46526200	Weak transcription	Ovary	ovary
40	chr21:46524800-46526400	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr21:46524800-46527800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr21:46524800-46528400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr21:46524800-46528400	Weak transcription	Lung	lung
44	chr21:46524800-46528800	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr21:46524800-46528800	Weak transcription	Spleen	Spleen
46	chr21:46524800-46528800	Weak transcription	Monocytes-CD14+_RO01746	blood
47	chr21:46524800-46529000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr21:46524800-46529000	Weak transcription	Gastric	stomach
49	chr21:46524800-46529000	Weak transcription	Pancreas	Pancrea
50	chr21:46524800-46529400	Enhancers	Primary B cells from peripheral blood	blood

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